Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Protein and Protein Interactions
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Protein and Protein Interactions

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 May 2025 | Viewed by 4699

Special Issue Editor

Dr. Wu Xu

grade E-Mail Website
Guest Editor
Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, USA
Interests: gene expression; DNA-binding transcription factors; cell growth

Special Issue Information

Dear Colleagues,

Proteins play a vital role in sustaining life, requiring the formation of specific 3D structures to manifest their essential biological functions. Life is about relationships between molecules, not a property of any single molecule. Among the pivotal elements contributing to various processes are noncovalent interactions, which include protein-protein, protein-DNA/RNA, ligand-receptor, drug-target, or host-guest interactions. Determining molecular interactions can be achieved through structural and experimental methods like X-ray crystallography, NMR or Cryo-EM techniques. Functional assays, including yeast-two hybrid, pulldown experiment, or FRET method, conducted in laboratory settings, can also provide evidence of these interactions. It remains a formidable challenge to computationally predict these intricate molecular interactions. Physics-based methods for calculating binding free energy and empirical scoring functions for assessing binding affinities have been used to investigate protein-protein interactions. Nevertheless, the lack of a mechanistic understanding of molecular interactions poses a significant obstacle to computationally identify binding partners and to elucidate the corresponding regulatory mechanisms governing their functions.

This Special Issue for IJMS aims at gathering contributions with the focus on improving the mechanistic understanding of protein and protein interactions including ligand and protein interactions using computational approaches. Development of new computational methods or software tools are encouraged.

Dr. Wu Xu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein and protein interactions
  • ligand and protein interactions
  • computational method
  • geometry-based
  • energy-based
  • conformational changes
  • binding site prediction
  • structural biology
  • computational biology and bioinformatics

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

16 pages, 15521 KiB  
Article
Contrasting Effects of Platelet GPVI Deletion Versus Syk Inhibition on Mouse Jugular Vein Puncture Wound Structure
by Irina D. Pokrovskaya, Kelly K. Ball, Michael W. Webb, Smita Joshi, Sung W. Rhee, Jerry Ware and Brian Storrie
Int. J. Mol. Sci. 2025, 26(9), 4294; https://doi.org/10.3390/ijms26094294 - 1 May 2025
Viewed by 73
Abstract
Platelet glycoprotein (GP)VI is a transmembrane protein that was originally characterized as a collagen receptor supporting platelet adhesion and activation through its association with the Fc receptor γ-chain (FcRγ). The FcRγ subunit contains immunoreceptor tyrosine-based activation motifs (ITAMs) that recruit and activate Syk [...] Read more.
Platelet glycoprotein (GP)VI is a transmembrane protein that was originally characterized as a collagen receptor supporting platelet adhesion and activation through its association with the Fc receptor γ-chain (FcRγ). The FcRγ subunit contains immunoreceptor tyrosine-based activation motifs (ITAMs) that recruit and activate Syk (spleen tyrosine kinase), a key player in intracellular signaling pathways. The absence or dysfunction of GPVI produces a mild bleeding defect in humans like the impaired hemostasis reported in the murine knockout. Here, we took an ultrastructure approach to examine the impact of ligand binding to GPVI versus the downstream pharmacologic inhibition of the GPVI-dependent ITAM signaling pathway. Clots were generated for analysis following a puncture wound in the mouse external jugular vein. Images were obtained using mice genetically missing GPVI and mice pretreated with the Syk inhibitor, BI 1002494. Our study was designed to test the hypothesis that the predominant contribution of GPVI to hemostasis is mediated by a Syk-dependent signaling cascade. If true, the clot structure observed with a Syk inhibitor versus the GPVI knockout would be similar. If the extracellular domains of the protein had a Syk-independent platelet adhesion role, then significant comparative differences in the thrombus structure would be expected. Our results clearly indicate an important, Syk-independent role of the GPVI extracellular domain in the adherence of platelets within the intravascular crown of a growing venous clot, a site distant from exposed collagen-rich adventitia. In striking contrast, the adventitial proximal role of GPVI was Syk-dependent, with the GPVI knockout and Syk inhibitor giving the same, limited structural outcome of collagen-proximal platelet cytosol loss and a thinned extravascular cap. Consistent with the lesser role of Syk-dependent processes on the thrombus structure, the Syk inhibitor had no detectable effect on jugular puncture wound bleeding times, while the knockout had a statistically significant, but modest effect on bleeding time. Based on this contrast, we suggest that Syk inhibition may be the more selective approach to modulating the role of GPVI in occlusive clotting. Full article
(This article belongs to the Special Issue Protein and Protein Interactions)
►▼ Show Figures

Figure 1

11 pages, 5447 KiB  
Article
Molecular Dynamics Simulations Suggest That Side-Chain Motions of Charged Amino Acids Determine Long-Range Effects in Proteins: An Egg of Coulomb
by Neri Niccolai, Edoardo Morandi and Andrea Bernini
Int. J. Mol. Sci. 2024, 25(24), 13375; https://doi.org/10.3390/ijms252413375 - 13 Dec 2024
Cited by 1 | Viewed by 865
Abstract
Living systems cannot rely on random intermolecular approaches toward cell crowding, and hidden mechanisms must be present to favor only those molecular interactions required explicitly by the biological function. Electromagnetic messaging among proteins is proposed from the observation that charged amino acids located [...] Read more.
Living systems cannot rely on random intermolecular approaches toward cell crowding, and hidden mechanisms must be present to favor only those molecular interactions required explicitly by the biological function. Electromagnetic messaging among proteins is proposed from the observation that charged amino acids located on the protein surface are mostly in adjacent sequence positions and/or in spatial proximity. Molecular dynamics (MD) simulations have been used to predict electric charge proximities arising from concerted motions of charged amino acid side chains in two protein model systems, human ubiquitin and the chitinolytic enzyme from Ostrinia furnacalis. This choice has been made for their large difference in size and sociality. Protein electrodynamics seems to emerge as the framework for a deeper understanding of the long-distance interactions of proteins with their molecular environment. Our findings will be valuable in orienting the design of proteins with specific recognition patterns. Full article
(This article belongs to the Special Issue Protein and Protein Interactions)
►▼ Show Figures

Figure 1

Review

Jump to: Research

21 pages, 5723 KiB  
Review
The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria
by Miroslava Stastna
Int. J. Mol. Sci. 2024, 25(16), 8564; https://doi.org/10.3390/ijms25168564 - 6 Aug 2024
Cited by 2 | Viewed by 3272
Abstract
Probiotics can affect human health, keep the balance between beneficial and pathogenic bacteria, and their colonizing abilities enable the enhancement of the epithelial barrier, preventing the invasion of pathogens. Health benefits of probiotics were related to allergy, depression, eczema, cancer, obesity, inflammatory diseases, [...] Read more.
Probiotics can affect human health, keep the balance between beneficial and pathogenic bacteria, and their colonizing abilities enable the enhancement of the epithelial barrier, preventing the invasion of pathogens. Health benefits of probiotics were related to allergy, depression, eczema, cancer, obesity, inflammatory diseases, viral infections, and immune regulation. Probiotic bacterial cells contain various proteins that function as effector molecules, and explaining their roles in probiotic actions is a key to developing efficient and targeted treatments for various disorders. Systematic proteomic studies of probiotic proteins (probioproteomics) can provide information about the type of proteins involved, their expression levels, and the pathological changes. Advanced proteomic methods with mass spectrometry instrumentation and bioinformatics can point out potential candidates of next-generation probiotics that are regulated under pharmaceutical frameworks. In addition, the application of proteomics with other omics methods creates a powerful tool that can expand our understanding about diverse probiotic functionality. In this review, proteomic strategies for identification/quantitation of the proteins in probiotic bacteria were overviewed. The types of probiotic proteins investigated by proteomics were described, such as intracellular proteins, surface proteins, secreted proteins, and the proteins of extracellular vesicles. Examples of pathological conditions in which probiotic bacteria played crucial roles were discussed. Full article
(This article belongs to the Special Issue Protein and Protein Interactions)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop